- Open Access
Phylogenomics of Colombian Helicobacter pylori isolates
© The Author(s) 2017
- Received: 5 May 2017
- Accepted: 3 September 2017
- Published: 11 September 2017
During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori. Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H. pylori isolates.
A total of 115 genomes of H. pylori were sequenced with Illumina technology from H. pylori isolates obtained in Colombia in a region of high risk for gastric cancer. The genomes were assembled, annotated and underwent phylogenomic analysis with 36 reference strains. Additionally, population differentiation analyses were performed for two bacterial genes. The phylogenetic tree revealed clustering of the Colombian strains with hspWestAfrica and hpEurope, along with three clades formed exclusively by Colombian strains, suggesting the presence of independent evolutionary lines for Colombia. Additionally, the nucleotide diversity of horB and vacA genes from Colombian isolates was lower than in the reference strains and showed a significant genetic differentiation supporting the hypothesis of independent clades with recent evolution.
The presence of specific lineages suggest the existence of an hspColombia subtype that emerged from a small and relatively isolated ancestral population that accompanied crossbreeding of human population in Colombia.
- Helicobacter pylori
- Phylogenomic analysis
- Whole genome sequence
Helicobacter pylori infects 50% of the global population [1, 2] and is the aetiological agent of gastritis, peptic ulcer and stomach cancer [3, 4]. In general, the infection shows intrafamilial spread and is acquired during childhood and established throughout the life of the host . Chronic active gastritis is caused by the bacteria in all infected subjects; between 10 and 15% of cases progress to peptic ulcer, chronic atrophic gastritis, intestinal metaplasia, gastric dysplasia and cancer or to mucosa-associated lymphoid tissue lymphoma .
Helicobacter pylori has coevolved along with humans since their migration outside of Africa approximately 60,000 years ago . Multi-locus sequence typing (MLST) studies have shown the modern H. pylori strains to cluster into different regional populations based on their geographic origin: hpEurope, hpNEAfrica, hpAfrica1, hpAfrica2, hpAsia2, hpSahul and hpEastAsia; hpEastAsia is divided into three subpopulations, hspEAsia, hspMaori and hspAmerind [8–12]. The hspAmerind subpopulation reflects the migration from Asia to the Americas through the Bering Strait that started 12,000 years ago . A much more recent human migration event is the Spanish colonisation of the Americas 500 years ago. During this period, in addition to the Spanish, African slaves also migrated to the American continent. These migrations exposed the native population to new pathogens, including new strains of H. pylori, which led to the disappearance of 80% of the native population in the subsequent decades [14, 15].
Multi-locus sequence typing studies of urban H. pylori isolates from Colombia have shown that the strains are mainly of the hpEurope type and, in a lower proportion, of the hpAfrica type; the latter type has been found mainly in the Afro-American population living along the coast [16–18]. Similarly to other regions of Latin America, the native strains of the Amerindian populations in Colombia were displaced by European strains in the mestizo population descended from the Amerindians and the Spanish population that arrived on the continent during the Spanish colonisation [16–21].
Helicobacter pylori is a bacterium that can display very fast local adaptive processes via mutation and homologous recombination with other strains [22, 23]. These characteristics are evidenced in the study of Shiota et al. , who described the existence of a specific population component in strains isolated from the Colombian mestizo population, which suggests that despite their European origin, these strains are clearly differentiated within this population. Recent whole-genome sequence-based studies have shown that in Nicaragua, Mexico and Colombia, H. pylori strains have followed unique evolutionary pathways ; and that in Colombia, bacterial populations evolve quickly and have formed new subpopulations from a European source . These findings highlight the need for thorough phylogenomic studies to describe the population structure of the Colombian isolates of H. pylori.
Helicobacter pylori has species-specific genes that are useful as population markers to explore genetic differentiation among strains; among them are horB gene, a member of the outer membrane proteins family of Helicobacter pylori  that encodes a 30-kDa adhesin essential for the tropism of the bacteria towards human gastric epithelium , and the vacA gene, one of the major virulence factors of the bacterium, that encodes the cytotoxin VacA, which is a factor that induces apoptosis, increases the permeability of gastric cells and suppresses the immune response, among other effects .
A total of 103 genomes of H. pylori isolates from Colombia were characterised in this study. Phylogenomic and population analyses were performed. The phylogenomic reconstruction allowed the identification of strains associated with both hpEurope and hspWAfrica and, at the same time, the proposal of a new subpopulation, hspColombia, composed of novel genomes.
Bacterial culture and DNA isolation
Gastric pathologies of patients
Number (% of total)
Gastritis and duodenal ulcer (G–DU)
Atrophic gastritis (AG)
Intestinal metaplasia (IM)
Intestinal metaplasia and duodenal ulcer IM–DU
Gastric adenocarcinoma (GA)
Library preparation and genome sequencing
Libraries were prepared using a Nextera XT DNA Sample Preparation Kit (Illumina, San Diego, CA, USA) with 1 ng of DNA according to the manufacturer’s protocol (Nextera XT protocol, Version October 2012) and sequenced using a MiSeq Personal Sequencer (Illumina, San Diego, CA, USA). Sequencing reactions were performed using MiSeq v2. Chemistry (Illumina, San Diego, CA, USA).
Genome assembly and annotation
The readings were processed to remove adapters and low-quality regions. Then, reading errors were corrected using the SGA algorithm . The contigs were assembled using the IDBA-UD algorithm , and the scaffolds were assembled using the SSPACE tool . These programs were used according to the instructions of the A5-miseq pipeline , which was developed specifically for the Illumina platform and for small genomes of haploid organisms. Finally, the genomes were annotated in RAST .
Multi-locus sequence typing (MLST) analysis
The 103 genomes of Colombian isolates were annotated using http://pubmlst.org/helicobacter. Concatenated nucleotide sequences of seven housekeeping genes atpA, efp, mutY, ppa, trpC, ureI, and yphC from 103 Colombian isolates, and 163 reference were downloaded from the PubMLST database. The reference sequences were: hpEurope: 82 sequences; hpAfrica1: 16 sequences; hpWestAfrica: 23 sequences; hspSouthIndia: 2 sequences; hpEastAsia: 8 sequences; and hspAmerind: 7 sequences. The concatenated nucleotide sequences were aligned using Muscle software . Phylogenetic analyses were conducted in Mega V7 using T92+G+I (Tamura model with Gamma function and Invariable sites) . Bootstrap analysis was performed with 1000 replications, and Phylogenetic tree was edited with iTol v3 .
The genomes sequenced in this study were aligned with 34 H. pylori reference strains from the National Center for Biotechnology Information (NCBI) databases using the Gegenees v2.21 tool. This tool uses an algorithm to align genomic fragments and compares them by Blastn [36, 37]. The fragment size was 200 bp, and the sliding step size was 100 bp. The average sequence similarity was set at 40% to generate a genomic similarity matrix, which was then exported in.nex format. This file was analysed using Splitstree4 v4.14.5 software , which generated a rootless tree using the NJ algorithm. Then, the file was edited using iTool v3 software . The core genome SNP analysis was performed using the KSNP v3.0 program , this suit has been used for SNP identification and phylogenetic analysis of H. pylori strains . K-chooser tool was used to determine the k-mer value. It was 21 and 141 k-mers were indentified in the core. The final phylogenetic tree was a consensus between 100 parsimonious trees. Lastly, a gen cluster analysis was performed using the GET_HOMOLOGUES v3.06  to extract the horB and vacA genes for population analysis.
HorB and vacA virulence genes were used as population markers because they are present in most isolates, play key roles in the physiopathology of the infection and are species-specific. A total of 137 nucleotide sequences were obtained for each gene, and the sequences were aligned using the Muscle program . The files containing the alignments were analysed using MEGA 6.1 software , with which the evolutionary models were determined, and the phylogenetic reconstructions with 1000 bootstrap repetitions were performed using the NJ algorithm . In addition, Tajima’s D test  was performed to detect the effects of natural selection on the sequences. Due to the extreme diversity of the vacA gene, the Gblocks tool  was used to edit the alignment of this gene and to choose its most parsimonious regions.
The marker genes were divided into populations according to the pathology associated with the strain from which they were sequenced. To determine the genetic diversity of the markers, the following population statistics were obtained: number of haplotypes (H), haplotype diversity (Hd), nucleotide diversity (Pi) and average number of nucleotide differences (k). Genetic heterogeneity and genetic flow were evaluated using the Snn, GammaST and Fst tests in the DnaSP 5.10 software . Finally, heterogeneity tests were applied to population pairs.
A total of 115 H. pylori isolates were included in the study; twelve genomes showing low sequence quality were excluded. The 103 remaining genomes showed a mean of 85 contigs, 127× coverage, 1.65 MB in size, 39% G+C and 1647 genes (Additional file 1: Table S1).
Analysis of genetic diversity, differentiation and genetic flow in total populations
Col. and Ref.
Col. and Ref.
Pairwise analysis of genetic differentiation
G vs. hspAmerind
GA vs. hspAmerind
IM vs. hspAmerind
IGA vs. hspAmerind
DGA vs. hspAmerind
G/DU vs. hspAmerind
IM/DU vs. hspAmerind
G vs. HpEurope
GA vs. HpEurope
IM vs. HpEurope
IGA vs. HpEurope
DGA vs. HpEurope
G/DU vs. HpEurope
IM/DU vs. HpEurope
G vs. HpAsia
GA vs. HpAsia
IM vs. HpAsia
IGA vs. HpAsia
DGA vs. HpAsia
G/DU vs. HpAsia
IM/DU vs. HpAsia
G vs. HpAfrica
GA vs. HpAfrica
IM vs. HpAfrica
IGA vs. HpAfrica
DGA vs. HpAfrica
G/DU vs. HpAfrica
IM/DU vs. HpAfrica
The phylogenetic analysis based on the complete H. pylori genome showed that approximately half of the strains isolated from the Colombian mestizo population clustered with the hpEurope and hspWestAfrica clades. This finding was also reported in previous MLST studies conducted in this population [16–18], and represents the introduction of European strains by the Spanish during the conquest of America and of strains from the West of Africa due to the subsequent arrival of African slaves. The remaining strains analysed constituted three independent clades consisting exclusively of Colombian strains, suggesting the presence of independent evolutionary lines in the country. Mestizos have their own genetic components, which are relatively new in human history . The admixture between mestizos allowed the recombination of hpEurope type strains and their adaptation to a new host, generating the hspColombia subpopulation. This type of adaptive event has also been reported in Senegal .
The phylogenomic reconstruction revealed that the Colombian isolates are not related to hspAmerind type genomes; this finding is consistent with previous studies showing that no Asian components are found in the population structure of H. pylori [16–18]. Prior to colonisation, the region was dominated by hspAmerind strains, which arrived on the American continent through the Bering Strait . This subpopulation has been reported in Amerindians in Peru , Mexico, Venezuela and Colombia ; however, currently in urban mestizo populations the hspAmerind strains have been replaced by hpEurope strains [16–18, 49–52]. The new niche that emerged from the conquest was a mixture of haplotypes (European, Amerindian and African) that allowed competition among circulating strains and put the hspAmerind subpopulation at a disadvantage, ultimately causing it to disappear from the mestizo population.
The emergence of independent evolutionary lines for H. pylori in Colombia over a relatively short time, from the Spanish conquest in 1492 to the present, can be explained by the adaptive capacity of H. pylori. The population structure of the bacterium is panmictic and naturally competent, that is, the bacterium can take genetic material from the external environment, incorporate it into its genome and express it . In addition, H. pylori shows great genetic diversity: the gene content and order vary among strains, its genes have mosaic structures, and the most conserved genes are highly variable at the DNA sequence level . These features allow the bacteria to undergo rapid microevolutionary changes [22, 23, 54] generating new population subtypes such as those reported in Malaysia  and Arabia  and now in Colombia, where the hspColombia subtype is proposed.
The hspColombia subtype is also supported by the results of the phylogenetic and population analyses performed on horB and vacA virulence genes. The phylogenetic reconstruction of each gene indicated the presence of specific Colombian clades, suggesting the existence of independent evolutionary processes for the Colombian isolates. When the full populations were assessed for each marker, several features pointing to this conclusion were found: (1) low nucleotide diversity with high haplotype diversity was found; (2) high genetic differentiation with constant genetic flow was determined; (3) both genes showed areas under strong selective pressure, likely because these genes are immunogenic; and (4) the Colombian populations are significantly less diverse than the reference genomes. It is possible that Colombian strains may have evolved to be more virulent than the European ones, considering that vacA is an important virulence factor and that Colombian gastric cancer-associated strains differ from hpEurope in their vacA sequence. Further studies are warranted to test this possibility.
HspColombia is characterised by being genetically differentiated from the hspAmerind and hpAsia populations, showing an African component that has been assimilated during the evolutionary process and having as a common ancestor the hpEurope type.
MMB, AJG, and OA conceived the study, ETG generated the sequence data, AJG performed bioinformatics analysis, AJG, ETG and MMB participated in results analysis, AJG and MMB prepared the manuscript. All authors read and approved the final manuscript.
We gratefully acknowledge Luz Adriana Cifuentes for her excellent technical assistance in obtaining sequences.
The authors declare that they have no competing interests.
Availability of data and materials
The complete genomes of H. pylori have been deposited in Gen Bank under Accession Numbers PRJNA329330 to PRJNA329337 but restrictions apply to the availability of these data, and so are not publicly available until November 2017. Data are however available from the authors upon reasonable request.
Consent for publication
Ethics approval and consent to participate
The clinical studies where patients were originally recruited were approved by the Ethical and Research Committee of the Instituto Nacional de Cancerología, and all the patients signed an informed consent. This study was approved by the Ethical and Research Committee of the Instituto Nacional de Cancerología.
This study was supported by Grants 41030610588 of Instituto Nacional de Cancerología to MM Bravo, and 599-2014 of Colciencias.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Perez-Perez GI, Rothenbacher D, Brenner H. Epidemiology of Helicobacter pylori infection. Helicobacter. 2004;9(Suppl 1):1–6.View ArticlePubMedGoogle Scholar
- Khalifa MM, Sharaf RR, Aziz RK. Helicobacter pylori: a poor man’s gut pathogen? Gut Pathog. 2010;2:2.View ArticlePubMedPubMed CentralGoogle Scholar
- Amieva MR, El-Omar EM. Host-bacterial interactions in Helicobacter pylori infection. Gastroenterology. 2008;134:306–23.View ArticlePubMedGoogle Scholar
- Cover TL, Blaser MJ. Helicobacter pylori in health and disease. Gastroenterology. 2009;136:1863–73.View ArticlePubMedPubMed CentralGoogle Scholar
- Fujimoto Y, Furusyo N, Toyoda K, Takeoka H, Sawayama Y, Hayashi J. Intrafamilial transmission of Helicobacter pylori among the population of endemic areas in Japan. Helicobacter. 2007;12:170–6.View ArticlePubMedGoogle Scholar
- Correa P, Piazuelo MB. The gastric precancerous cascade. J Dig Dis. 2012;13:2–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature. 2007;445:915–8.View ArticlePubMedPubMed CentralGoogle Scholar
- Achtman M, Azuma T, Berg DE, Ito Y, Morelli G, Pan ZJ, et al. Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol Microbiol. 1999;32:459–70.View ArticlePubMedGoogle Scholar
- Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, et al. Traces of human migrations in Helicobacter pylori populations. Science. 2003;299:1582–5.View ArticlePubMedGoogle Scholar
- Moodley Y, Linz B, Yamaoka Y, Windsor HM, Breurec S, Wu JY, et al. The peopling of the Pacific from a bacterial perspective. Science. 2009;323:527–30.View ArticlePubMedPubMed CentralGoogle Scholar
- Devi SM, Ahmed I, Francalacci P, Hussain MA, Akhter Y, Alvi A, et al. Ancestral European roots of Helicobacter pylori in India. BMC Genom. 2007;8:184.View ArticleGoogle Scholar
- Yamaoka Y. Helicobacter pylori typing as a tool for tracking human migration. Clin Microbiol Infect. 2009;15:829–34.View ArticlePubMedPubMed CentralGoogle Scholar
- Kersulyte D, Kalia A, Gilman RH, Mendez M, Herrera P, Cabrera L, et al. Helicobacter pylori from Peruvian amerindians: traces of human migrations in strains from remote Amazon, and genome sequence of an Amerind strain. PLoS ONE. 2010;5:e15076.View ArticlePubMedPubMed CentralGoogle Scholar
- Bianchine PJ, Russo TA. The role of epidemic infectious diseases in the discovery of America. Allergy Proc. 1992;13:225–32.View ArticlePubMedGoogle Scholar
- Parrish CR, Holmes EC, Morens DM, Park EC, Burke DS, Calisher CH, et al. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol Mol Biol Rev. 2008;72:457–70.View ArticlePubMedPubMed CentralGoogle Scholar
- de Sablet T, Piazuelo MB, Shaffer CL, Schneider BG, Asim M, Chaturvedi R, et al. Phylogeographic origin of Helicobacter pylori is a determinant of gastric cancer risk. Gut. 2011;60:1189–95.View ArticlePubMedPubMed CentralGoogle Scholar
- Shiota S, Suzuki R, Matsuo Y, Miftahussurur M, Tran TT, Binh TT, et al. Helicobacter pylori from gastric cancer and duodenal ulcer show same phylogeographic origin in the Andean region in Colombia. PLoS ONE. 2014;9:e105392.View ArticlePubMedPubMed CentralGoogle Scholar
- Munoz-Ramirez ZY, Mendez-Tenorio A, Kato I, Bravo MM, Rizzato C, Thorell K, et al. Whole genome sequence and phylogenetic analysis show Helicobacter pylori strains from latin America have followed a unique evolution pathway. Front Cell Infect Microbiol. 2017;7:50.View ArticlePubMedPubMed CentralGoogle Scholar
- Kodaman N, Pazos A, Schneider BG, Piazuelo MB, Mera R, Sobota RS, et al. Human and Helicobacter pylori coevolution shapes the risk of gastric disease. Proc Natl Acad Sci USA. 2014;111:1455–60.View ArticlePubMedPubMed CentralGoogle Scholar
- Dominguez-Bello MG, Perez ME, Bortolini MC, Salzano FM, Pericchi LR, Zambrano-Guzman O, et al. Amerindian Helicobacter pylori strains go extinct, as european strains expand their host range. PLoS ONE. 2008;3:e3307.View ArticlePubMedPubMed CentralGoogle Scholar
- Suzuki R, Shiota S, Yamaoka Y. Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. Infect Genet Evol. 2012;12:203–13.View ArticlePubMedGoogle Scholar
- Furuta Y, Konno M, Osaki T, Yonezawa H, Ishige T, Imai M, et al. Microevolution of virulence-related genes in Helicobacter pylori familial infection. PLoS ONE. 2015;10:e0127197.View ArticlePubMedPubMed CentralGoogle Scholar
- Cao Q, Didelot X, Wu Z, Li Z, He L, Li Y, et al. Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. Gut. 2015;64:554–61.View ArticlePubMedGoogle Scholar
- Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, et al. Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. PLoS Genet. 2017;13:e1006546.View ArticlePubMedPubMed CentralGoogle Scholar
- Matsuo Y, Kido Y, Yamaoka Y. Helicobacter pylori outer membrane protein-related pathogenesis. Toxins (Basel). 2017;9:101.View ArticlePubMed CentralGoogle Scholar
- Snelling WJ, Moran AP, Ryan KA, Scully P, McGourty K, Cooney JC, et al. HorB (HP0127) is a gastric epithelial cell adhesin. Helicobacter. 2007;12:200–9.View ArticlePubMedGoogle Scholar
- Jones KR, Whitmire JM, Merrell DS. A tale of two toxins: Helicobacter pylori CagA and VacA modulate host pathways that impact disease. Front Microbiol. 2010;1:115.View ArticlePubMedPubMed CentralGoogle Scholar
- Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012;22:549–56.View ArticlePubMedPubMed CentralGoogle Scholar
- Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.View ArticlePubMedGoogle Scholar
- Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27:578–9.View ArticlePubMedGoogle Scholar
- Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2015;31:587–9.View ArticlePubMedGoogle Scholar
- Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2014;42:D206–14.View ArticlePubMedGoogle Scholar
- Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5.View ArticlePubMedPubMed CentralGoogle Scholar
- Agren J, Sundstrom A, Hafstrom T, Segerman B. Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS ONE. 2012;7:e39107.View ArticlePubMedPubMed CentralGoogle Scholar
- Kumar N, Mukhopadhyay AK, Patra R, De R, Baddam R, Shaik S, et al. Next-generation sequencing and de novo assembly, genome organization, and comparative genomic analyses of the genomes of two Helicobacter pylori isolates from duodenal ulcer patients in India. J Bacteriol. 2012;194:5963–4.View ArticlePubMedPubMed CentralGoogle Scholar
- Huson DH. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 1998;14:68–73.View ArticlePubMedGoogle Scholar
- Gardner SN, Slezak T, Hall BG. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics. 2015;31:2877–8.View ArticlePubMedGoogle Scholar
- van Vliet AH, Kusters JG. Use of alignment-free phylogenetics for rapid genome sequence-based typing of Helicobacter pylori virulence markers and antibiotic susceptibility. J Clin Microbiol. 2015;53:2877–88.View ArticlePubMedPubMed CentralGoogle Scholar
- Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013;79:7696–701.View ArticlePubMedPubMed CentralGoogle Scholar
- Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.PubMedGoogle Scholar
- Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.PubMedPubMed CentralGoogle Scholar
- Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56:564–77.View ArticlePubMedGoogle Scholar
- Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451–2.View ArticlePubMedGoogle Scholar
- Ruiz-Linares A, Adhikari K, Acuna-Alonzo V, Quinto-Sanchez M, Jaramillo C, Arias W, et al. Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7342 individuals. PLoS Genet. 2014;10:e1004572.View ArticlePubMedPubMed CentralGoogle Scholar
- Linz B, Vololonantenainab CR, Seck A, Carod JF, Dia D, Garin B, et al. Population genetic structure and isolation by distance of Helicobacter pylori in Senegal and Madagascar. PLoS ONE. 2014;9:e87355.View ArticlePubMedPubMed CentralGoogle Scholar
- O’Rourke DH. Human migrations: the two roads taken. Curr Biol. 2009;19:R203–5.View ArticlePubMedGoogle Scholar
- Camorlinga-Ponce M, Perez-Perez G, Gonzalez-Valencia G, Mendoza I, Penaloza-Espinosa R, Ramos I, et al. Helicobacter pylori genotyping from American indigenous groups shows novel Amerindian vacA and cagA alleles and Asian, African and European admixture. PLoS ONE. 2011;6:e27212.View ArticlePubMedPubMed CentralGoogle Scholar
- Sicinschi LA, Correa P, Peek RM, Camargo MC, Piazuelo MB, Romero-Gallo J, et al. CagA C-terminal variations in Helicobacter pylori strains from Colombian patients with gastric precancerous lesions. Clin Microbiol Infect. 2010;16:369–78.View ArticlePubMedGoogle Scholar
- Thorell K, Hosseini S, Palacios Gonzales RV, Chaotham C, Graham DY, Paszat L, et al. Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua. BMC Evol Biol. 2016;16:53.View ArticlePubMedPubMed CentralGoogle Scholar
- Yamaoka Y, Orito E, Mizokami M, Gutierrez O, Saitou N, Kodama T, et al. Helicobacter pylori in North and South America before Columbus. FEBS Lett. 2002;517:180–4.View ArticlePubMedGoogle Scholar
- Noto JM, Peek RM Jr. Genetic manipulation of a naturally competent bacterium, Helicobacter pylori. Methods Mol Biol. 2012;921:51–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Suzuki M, Kiga K, Kersulyte D, Cok J, Hooper CC, Mimuro H, et al. Attenuated CagA oncoprotein in Helicobacter pylori from Amerindians in Peruvian Amazon. J Biol Chem. 2011;286:29964–72.View ArticlePubMedPubMed CentralGoogle Scholar
- Kumar N, Mariappan V, Baddam R, Lankapalli AK, Shaik S, Goh KL, et al. Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution. Nucleic Acids Res. 2015;43:324–35.View ArticlePubMedGoogle Scholar
- Kumar N, Albert MJ, Al AH, Siddique I, Ahmed N. What constitutes an Arabian Helicobacter pylori? Lessons from comparative genomics. Helicobacter. 2016;22:1–11.Google Scholar